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refmesh

A hybrid knowledge-graph CLI for autonomous coding agents (Claude Code, OpenAI Codex CLI, etc.). Extracts "concepts (nodes)" and "relationships (edges)" from official docs and references, stores them in a single-file SQLite database, and serves vector semantic search + BM25 full-text search + graph traversal — all from one process.

• Storage: better-sqlite3 single DB file (~/.refmesh/refmesh.db), with PRAGMA journal_mode=WAL and foreign keys enabled.
• Vector index: In-memory Float32Array with normalized cosine similarity, hydrated from SQLite at startup.
• Full-text: SQLite FTS5 (Okapi BM25) with the multilingual unicode61 remove_diacritics 2 tokenizer.
• Graph traversal: BFS over the edges table, expanded depth levels per public edge type.
• Embeddings: @xenova/transformers + Xenova/paraphrase-multilingual-MiniLM-L12-v2 (multilingual, 384-dim). Vectors are generated inside the Node.js process — no Python dependency.

Installation

For users (use as a CLI)

Install globally from npm:

npm install -g refmesh
refmesh --help
refmesh types          # smoke test

Important

Note for existing users (storage unified to SQLite in PBI-18): Older versions used Kùzu + LanceDB at ~/.refmesh/graph.kuzu and ~/.refmesh/vectors.lance. There is no compatibility with that data — after upgrading, delete both directories and re-run refmesh register. The new database lives in a single file at ~/.refmesh/refmesh.db.

better-sqlite3 requires a native build, but prebuilt binaries are published for major OS / Node.js combinations, so plain npm install usually works without a toolchain.

On the first refmesh search, the multilingual embedding model (~80 MB) is downloaded from the Hugging Face Hub to ~/.refmesh/models/. After that, refmesh runs offline.

When invoking refmesh from a sandboxed CLI with restricted write access (e.g., Codex CLI), writes to ~/.refmesh/models/ will fail and the model loader will hang. Pre-populate the cache with refmesh prefetch from a user that can write — subsequent refmesh search / register will then run read-only against the cache. Override the location with the REFMESH_MODEL_DIR environment variable (pass the same value at prefetch time and at runtime).

For developers (working in this repo)

mise install      # fetch the Node.js 22 (arm64) version pinned in mise.toml
npm install
npm run build
npm run dev -- types          # run directly via tsx
# or expose your local build globally
npm link && refmesh --help

Usage

1. Inspect the schema and edge types

refmesh types
# or as machine-readable JSON
refmesh types --format json

2. Register knowledge

Pipe JSON in:

cat knowledge.json | refmesh register

Or pass a file path:

refmesh register -f knowledge.json

Example payload (publishedAt / fetchedAt are optional, but strongly recommended if you plan to use freshness scoring):

{
  "reference": {
    "url": "https://react.dev/reference/react/hooks",
    "title": "Built-in React Hooks",
    "publishedAt": "2026-04-01T00:00:00Z",
    "fetchedAt": "2026-04-26T00:00:00Z"
  },
  "concepts": [
    {
      "id": "useState",
      "description": "A Hook that lets you add a state variable to a component.",
      "details": "const [state, setState] = useState(initialState);"
    },
    { "id": "React Hooks", "description": "Built-in hooks for React state and lifecycle features." }
  ],
  "relationships": [
    {
      "source": "useState",
      "target": "React Hooks",
      "type": "PART_OF",
      "reason": "useState is one of the standard hooks shipped by React."
    }
  ]
}

Re-running register updates the concept's lastSeenAt and increments touchCount automatically (firstSeenAt is preserved).

3. Search

Queries are natural language. They are embedded, used to pick seed concepts, then expanded --depth levels through the graph to return a related cluster of knowledge.

refmesh search "Safe state management in React"           # natural-language query → semantic search → depth=1 expansion
refmesh search "React Hooks" --depth 2 --limit 10         # walk 2 hops, take up to 10 vector candidates
refmesh search "useState" --threshold 0.7 --format json   # only similarity ≥ 0.7, JSON output

Options:

• --depth <n>: graph traversal depth (default: 1)
• --limit <n>: maximum number of seed candidates from vector search (default: 5)
• --threshold <value>: minimum similarity threshold, [0, 1] (default: 0.3)
• --freshness-weight <0..1>: weight of freshness in the final score (default: 0 — freshness ignored)
• --half-life <days>: freshness half-life (default: 180)
• --max-age <days>: drop nodes older than this from results (default: unlimited)
• --demote-deprecated <0..1>: multiplier applied to targets of DEPRECATES / REPLACES (default: 0.5; use 0 to exclude)
• --reinforcement-weight <0..1>: weight of access-count reinforcement (default: 0; freshness + reinforcement ≤ 1)
• --lexical-weight <0..1>: lexical boost from token overlap against id / description / details (default: 0.3; independent of cosine)
• --bm25-weight <0..1>: full-text boost from SQLite FTS5 / BM25 (default: 0.3; independent of cosine)
• --include-archived: include archived nodes in results
• --format <text|json>: output format (default: text)

The final score is final = max(0, 1 − w_f − w_r − w_l − w_b) · cosine + w_f · freshness + w_r · reinforcement + w_l · lexical + w_b · bm25 (multiplied additionally by demoteDeprecated when the candidate is demoted). The candidate set is the union of vector top-K and FTS5 top-K, merged per concept and re-ranked, so concepts that only one retriever surfaces are still picked up. freshness = exp(−ln2 · age / halfLife), where age is computed from the latest Reference.publishedAt (falling back to Concept.lastSeenAt).

Duplicate detection at registration

register compares each new concept's embedding against the existing vector index. If any existing node has similarity ≥ 0.95, the run prints ⚠ Similar existing concepts in the summary. Agents should treat this as a signal to stop creating a new node and instead reuse the existing id, or connect the two with a SAME_AS edge.

4. Inspect the graph in the browser (refmesh console)

refmesh console starts a local web dashboard so you can visually inspect the graph. It is read-only and accepts loopback (127.0.0.1) connections only. There are no Python dependencies.

refmesh console                # bind to a free port and open the default browser
refmesh console --port 8765    # pin a port
refmesh console --no-open      # just print the URL, don't launch a browser

Dashboard tabs:

• Overview: counts of Concepts / References / Edges, edge-type distribution, plus the SQLite DB path, file size, and vector row count.
• Concepts: paginated list with sorting (lastSeenAt / touchCount / id); archived rows can be toggled in.
• Search: run the same scored search as refmesh search against natural-language queries.
• Search Debug: stage-by-stage view of the search pipeline — query embedding shape (dim / L2 norm / full-vector preview), the oversample / threshold settings sent to the vector index along with all vector hits before threshold filtering (including rejected ones), the SQL queries issued to the graph during traversal, the per-candidate score breakdown (cosine / freshness / reinforcement / lexical / bm25 / final and any exclusion reason), and per-level frontier and added-edge counts. Read-only — does not bump accessCount.
• Graph: pick a seed concept and render the graph. Click a node to expand its neighborhood incrementally; edges are color-coded by edge type.

Ctrl+C stops the server and cleanly closes the SQLite handle (statement cache + db).

5. Curate stale knowledge (archive / prune)

# Logical archive — excluded from search, recoverable
refmesh archive OldUseState --reason "replaced by hooks"
refmesh unarchive OldUseState

# Physical delete — dry-run by default
refmesh prune --older-than 365 --max-touches 1
refmesh prune --older-than 365 --max-touches 1 --apply

prune deletes concepts whose lastSeenAt is older than the cutoff and whose touchCount is <= --max-touches, removing them from both the concept tables and the vector index. By default archived concepts are excluded; pass --include-archived to include them. Nothing is changed unless --apply is given.

Driving refmesh from agents (bundled skills)

example/skills/ ships three skills that work for both Claude Code and OpenAI Codex CLI. Each is triggered by a different scenario; copy the folder into ~/.claude/skills/ or ~/.codex/skills/ to start using them.

Skill	Trigger	What it does
refmesh-register	"Analyze this URL and remember it", "remember this doc"	Fetch URL → extract concepts → discover existing graph via refmesh search → connect to existing nodes with edges and call refmesh register
refmesh-search	At task start, the moment a proper noun or goal appears	Natural-language semantic search + multi-seed BFS, with a situational flag table for freshness / demote / reinforcement
refmesh-curate	On a ⚠ Similar existing concepts warning, generational handoff, stale-knowledge cleanup	Decision tree for SAME_AS merge / REPLACES / DEPRECATES / archive / prune

Each skill is a SKILL.md (shared by Claude and Codex) plus agents/openai.yaml (Codex UI metadata).

Installation

# Claude Code (project-scoped)
mkdir -p .claude/skills && cp -r example/skills/refmesh-* .claude/skills/

# Claude Code (user-wide)
mkdir -p ~/.claude/skills && cp -r example/skills/refmesh-* ~/.claude/skills/

# OpenAI Codex CLI
mkdir -p ~/.codex/skills && cp -r example/skills/refmesh-* ~/.codex/skills/

Once installed, prompts like "Read this URL and remember it" or "Tell me about the React Hooks I just registered" will match the skill's description triggers and invoke the corresponding skill, which in turn calls the refmesh CLI.

Storage paths

• DB (SQLite) — default: ~/.refmesh/refmesh.db / override: REFMESH_DB_PATH
• Embedding model cache — default: ~/.refmesh/models/ / override: REFMESH_MODEL_DIR

The embedding model cache is created automatically on the first refmesh search / register, or can be populated explicitly via refmesh prefetch (useful for permission-restricted runtimes):

refmesh prefetch                      # populate ~/.refmesh/models/ (skipped if already present)
refmesh prefetch --format json        # machine-readable output
REFMESH_MODEL_DIR=/opt/refmesh/models refmesh prefetch   # override the cache location

Edge types

15 public edge types are exposed (list them with refmesh types). Categories: structural / dependency / data flow / comparison / identity resolution / lifecycle.

SAME_AS (identity-resolution) connects two concepts that ended up as separate nodes due to naming variation but really refer to the same thing. DESCRIBES is reserved for the CLI's own Reference → Concept linking and is never written by users directly.

Development

npm run typecheck   # type checking
npm run lint        # static analysis with biome
npm run format      # format with biome
npm test            # run tests with vitest
npm run build       # compile to dist/

Architecture

src/
├── cli.ts                 # entry point (commander)
├── index.ts               # library exports
├── commands/
│   ├── types.ts           # refmesh types
│   ├── register.ts        # refmesh register (synchronized Concept + Vector + FTS updates)
│   ├── search.ts          # refmesh search (composite cosine + freshness + reinforcement + lexical + bm25 score)
│   ├── archive.ts         # refmesh archive / unarchive / prune
│   ├── console.ts         # refmesh console (local web dashboard)
│   └── prefetch.ts        # refmesh prefetch (embedding model pre-download / placement)
├── console/
│   ├── handlers.ts        # read-only API (stats / concepts / neighbors / search / search-debug)
│   ├── server.ts          # loopback-only HTTP server + static asset serving
│   └── index.ts
├── db/
│   ├── store.ts           # SQLite connection layer (better-sqlite3 + statement cache + WAL)
│   ├── migrations.ts      # schema DDL and migrations
│   ├── concept-repo.ts    # CRUD for Concept / Reference / Edge
│   ├── graph.ts           # BFS / frontier expansion over the edges table
│   ├── fts.ts             # FTS5 virtual table build + queries
│   ├── vector-index.ts    # in-memory Float32Array vector index
│   ├── statement-cache.ts # prepared-statement cache
│   └── paths.ts           # DB path resolution (~/.refmesh/refmesh.db, REFMESH_DB_PATH)
├── embedding/
│   ├── embedder.ts        # embedding generation via @xenova/transformers / prefetchEmbeddingModel()
│   └── paths.ts           # model cache path resolution (~/.refmesh/models/, REFMESH_MODEL_DIR)
├── schema/
│   ├── edge-types.ts      # edge enum + descriptions (single source of truth)
│   └── register-schema.ts # JSON Schema (for Ajv)
└── util/
    ├── errors.ts
    └── logger.ts

License

MIT